EvoWeb: EvoWeb: Predictions from EvoWeaver

In npcooley/SynExtend: Tools for Comparative Genomics

EvoWeb: Predictions from EvoWeaver

Description

EvoWeb objects can be returned from predict.EvoWeaver.

This class wraps the simMat object with some other diagnostic information intended to help interpret the output of EvoWeaver predictions.

Format

An object of class "EvoWeb", which inherits from "simMat".

Details

predict.EvoWeaver returns a EvoWeb object, which bundles some methods to make formatting and printing of results slightly nicer. This currently only implements a plot function.

Author(s)

Aidan Lakshman [e-mail]

See Also

predict.EvoWeaver

simMat

plot.EvoWeb

Examples

##############
## Prediction with built-in model and data
###############

exData <- get(data("ExampleStreptomycesData"))

# Subset isn't necessary but is faster for a working example
ew <- EvoWeaver(exData$Genes[1:10])

# default return value is a data.frame (recommended for most users)
evoweb <- predict(ew, Method='ExtantJaccard', ReturnDataFrame=FALSE)

# print out results as an adjacency matrix
print(evoweb)

# print out results as a pairwise data.frame
as.data.frame(evoweb)

npcooley/SynExtend documentation built on June 8, 2025, 5:24 a.m.